R/write.nii.voxel.R

In TKoscik/tk.nifti: Read and Write NIfTI Files

write.nii.voxel <- function(nii.file, coords, value) {
  # Check inputs ---------------------------------------------------------------
  stopifnot(!missing(nii.file), file.exists(nii.file),
            !missing(coords), !missing(value))

  # Get necessary NII file info ------------------------------------------------
  dims <- info.nii(nii.file, field="dim")[2:5]
  hdr <- info.nii(nii.file, field = c("vox_offset", "datatype", "bitpix"))

  # Check if coordinates are in range ------------------------------------------
  for (i in 1:length(coords)) { stopifnot(coords[i] <= dims[i]) }

  # Convert value to format from NII file --------------------------------------
  if (hdr$datatype %in% c(2,4,8,128,256,512,768,1024,1280)) {
    value <- as.integer(value)
  } else if (hdr$datatype %in% c(16, 32, 64)) {
    value <- as.double(value)
  } else {
    stop("Error converting value format")
  }

  # Calculate write location ---------------------------------------------------
  n <- length(coords)
  dimorder <- 1:n
  coords <- matrix(coords, nrow=1, ncol=length(coords))
  coords <- coords
  cdim <- cumprod(c(1, dims[dimorder][-n]))
  loc <- as.integer(colSums(t(coords[ , , drop=FALSE]-1) * cdim) + 1L)

  # Initialize NII file for binary reading and writing -------------------------
  fid <- file(nii.file, "r+b")
  endian <- .Platform$endian

  # Write value to file --------------------------------------------------------
  seek(fid,
       where=(hdr$vox_offset + (loc-1) * (hdr$bitpix/8)),
       origin="start",
       rw="write")

  # Write Value ----------------------------------------------------------------
  #switch(as.character(hdr$datatype),
  #       `2` = writeBin(value, fid, size=hdr$bitpix/8, endian=endian),
  #       `4` = writeBin(value, fid, size=hdr$bitpix/8, endian=endian),
  #       `8` = writeBin(value, fid, size=hdr$bitpix/8, endian=endian),
  #       `16` = writeBin(value, fid, size=hdr$bitpix/8, endian=endian),
  #       `64` = writeBin(value, fid, size=hdr$bitpix/8, endian=endian),
  #       stop("Error writing to file."))
  writeBin(value, fid, size=hdr$bitpix/8, endian=endian)
  close(fid)
}